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Yorodumi- PDB-6tyf: Crystal structure of MTB sigma L transcription initiation complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tyf | ||||||
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Title | Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA primer | ||||||
Components |
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Keywords | TRANSCRIPTION / tuberculosis / initiation / sigma finger displacement | ||||||
Function / homology | Function and homology information Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic ...Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Molodtsov, V. / Ebright, R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Authors: Li, L. / Molodtsov, V. / Lin, W. / Ebright, R.H. / Zhang, Y. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tyf.cif.gz | 710.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tyf.ent.gz | 517.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/6tyf ftp://data.pdbj.org/pub/pdb/validation_reports/ty/6tyf | HTTPS FTP |
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-Related structure data
Related structure data | 6konC 6kooC 6kopC 6koqC 6kqdC 6kqeC 6kqfC 6kqgC 6kqhC 6kqlC 6kqmC 6kqnC 6l74C 6ltsC 6tyeC 6tygC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 2 - 226 / Label seq-ID: 2 - 226
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 37745.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rpoA / Production host: Escherichia coli (E. coli) References: UniProt: A5U8D3, UniProt: P9WGZ1*PLUS, DNA-directed RNA polymerase #2: Protein | | Mass: 130018.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rpoB / Production host: Escherichia coli (E. coli) References: UniProt: P9WGY8, UniProt: P9WGY9*PLUS, DNA-directed RNA polymerase #3: Protein | | Mass: 146968.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: rpoC, rpoC_1, rpoC_2, DKC2_0716, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, EUB02_01475, EUB03_00860, EUB11_05575, SAMEA2682835_07420, SAMEA2682864_01702 Production host: Escherichia coli (E. coli) References: UniProt: A0A045J9E2, UniProt: P9WGY7*PLUS, DNA-directed RNA polymerase #4: Protein | | Mass: 11851.140 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_ ...Gene: rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_03677, ERS024213_01369, ERS024276_01577, ERS027644_00478, ERS027646_01439, ERS027651_03169, ERS027653_00843, ERS027659_01429, ERS027661_02200, ERS027666_04715, ERS031537_03443, EU767_08910, EU768_15085, EU769_05250, EU770_14555, EU771_05130, EU773_14340, EU774_06465, EU775_07590, EU776_17830, EU777_06800, EUB02_12495, EUB03_09550, EUB06_03645, EUB07_12165, EUB08_05285, EUB09_00425, EUB10_04215, EUB11_10790, EUB13_01060, EUB14_01055, EUB16_00425, SAMEA2682864_01599, SAMEA2683035_01133 Production host: Escherichia coli (E. coli) References: UniProt: A0A045H2R3, UniProt: P9WGY5*PLUS, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules GH
#5: DNA chain | Mass: 5885.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) |
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#6: DNA chain | Mass: 8373.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) |
-RNA chain / Protein , 2 types, 2 molecules IF
#7: RNA chain | Mass: 1851.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) |
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#8: Protein | Mass: 19563.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ...Gene: sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ERS024213_03781, ERS027644_01708, ERS027646_03649, ERS027651_00554, ERS027654_02031, ERS027659_03608, ERS027661_02428, ERS027666_03497, ERS031537_01383, ERS124361_02832, EU767_20440, EU768_17405, EU769_19535, EU770_10565, EU771_18640, EU773_15915, EU774_01235, EU775_01235, EU776_08285, EU777_18775, EUB02_13395, EUB03_01225, EUB07_01225, EUB08_01615, EUB09_12390, EUB10_16580, EUB11_05940, EUB12_18145, EUB13_14065, EUB14_03980, EUB16_03020, SAMEA2682835_06130, SAMEA2682864_01771, SAMEA2683035_02456 Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IR27, UniProt: P9WGH5*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, and 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.78→49.26 Å / Num. obs: 42516 / % possible obs: 95 % / Redundancy: 8.3 % / Biso Wilson estimate: 66.14 Å2 / CC1/2: 0.622 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.78→3.91 Å / Num. unique obs: 3902 / CC1/2: 0.622 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→49.26 Å / SU ML: 0.4855 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.0484
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→49.26 Å
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Refine LS restraints |
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LS refinement shell |
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